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Pairwise Alignment, Multiple Alignment, and BLAST
Quantitative comparison of sequences can be performed pairwise by aligning two sequences based on considerations of gaps representing insertions or...
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Pairwise Sequence Alignment
In a nutshell. A lot of bioinformatics consists of evaluating the similarity and differences between molecules, be they protein, RNA, or DNA...
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Protein embedding based alignment
PurposeDespite the many progresses with alignment algorithms, aligning divergent protein sequences with less than 20–35% pairwise identity (so called...
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An Algorithm for Pairwise DNA Sequences Alignment
A challenge in data analysis in bioinformatics is to offer integrated and modern access to the progressively increasing volume of data, as well as...
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Sensitive inference of alignment-safe intervals from biodiverse protein sequence clusters using EMERALD
Sequence alignments are the foundations of life science research, but most innovation so far focuses on optimal alignments, while information derived...
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Achieving quantitative reproducibility in label-free multisite DIA experiments through multirun alignment
DIA is a mainstream method for quantitative proteomics, but consistent quantification across multiple LC-MS/MS instruments remains a bottleneck in...
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Fast Alignment
We’ve seen that optimal alignment is slow but accurate while exact matching is fast but cannot account for mutations. In this Chapter we tweak exact...
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Alignment and integration of spatial transcriptomics data
Spatial transcriptomics (ST) measures mRNA expression across thousands of spots from a tissue slice while recording the two-dimensional (2D)...
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Optimal Alignment
When we align two sequences, we in fact propose an evolutionary history for them. A history, where we account for three kinds of events, mutation,...
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ACMGA: a reference-free multiple-genome alignment pipeline for plant species
BackgroundThe short-read whole-genome sequencing (WGS) approach has been widely applied to investigate the genomic variation in the natural...
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pmTM-align: scalable pairwise and multiple structure alignment with Apache Spark and OpenMP
BackgroundStructure comparison can provide useful information to identify functional and evolutionary relationship between proteins. With the...
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Gut microbial interactions based on network construction and bacterial pairwise cultivation
Association networks are widely applied for the prediction of bacterial interactions in studies of human gut microbiomes. However, the experimental...
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Multilayer network alignment based on topological assessment via embeddings
BackgroundNetwork graphs allow modelling the real world objects in terms of interactions. In a multilayer network, the interactions are distributed...
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Deep embedding and alignment of protein sequences
Protein sequence alignment is a key component of most bioinformatics pipelines to study the structures and functions of proteins. Aligning highly...
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Protein remote homology detection and structural alignment using deep learning
Exploiting sequence–structure–function relationships in biotechnology requires improved methods for aligning proteins that have low sequence...
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EMMA: a new method for computing multiple sequence alignments given a constraint subset alignment
BackgroundAdding sequences into an existing (possibly user-provided) alignment has multiple applications, including updating a large alignment with...
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Sequence Alignment
New biological sequences do not emerge de novo in nature but rather are derived from pre-existing sequences. This foundational principle underlies...
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Pairwise comparative analysis of six haplotype assembly methods based on users’ experience
BackgroundA haplotype is a set of DNA variants inherited together from one parent or chromosome. Haplotype information is useful for studying genetic...
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G-Aligner: a graph-based feature alignment method for untargeted LC–MS-based metabolomics
BackgroundLiquid chromatography–mass spectrometry is widely used in untargeted metabolomics for composition profiling. In multi-run analysis...
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Pairwise and Multi-chain Protein Docking Enhanced Using LZerD Web Server
Interactions of proteins with other macromolecules have important structural and functional roles in the basic processes of living cells. To...